In semiconductor manufacturing, semiconductor wafers must be safely transported between processing stations without damaging or destroying the wafers. The manufacturing of other articles (e.g., pharmaceuticals, medical systems, flat panel displays, computer hardware) may similarly require the careful handling and transport of materials. Semiconductor wafers may be retained in a clean room environment during processing to preserve the purity of the layers deposited on the wafers. For additional protection against contaminants, the semiconductor wafers may be retained in sealed transport containers as they are moved throughout the manufacturing facility in order to minimize any exposure to the environment outside of the processing stations. At various points during a fabrication process, semiconductor wafers may be transported in a container via an automated conveyor system, and the container may be temporarily removed from the conveyor system at various intervals to process the semiconductor wafers.